When using gnome-open/gvfs-open to open a file when nautilus is set as the default file manager, the file is not opened with the preferred application, instead nautilus is opens highlighting the file.
After some research I found this to be a bug yet to be fixed. But knowing that exo-open behaves properly, I came out a solution that's a little a hack: replace gnome-open and gvfs-open for exo-open.
Fix for YOUR USER only
As a prerequisite you should have a "bin" directory on your $HOME and it should be added to your $PATH. Them open a terminal window and run:
Fix for ALL USERS
Open a terminal window and run: